Molecular Modeling of Geochemical Reactions An Introduction

427 Pages·2016·17.713 MB·English

by  Kubicki, James David

Molecular Modeling of Geochemical Reactions
Dedication
To seea World in agrain of sand…
—William Blake
To my wife, Doris, and son, Cody, who bringmuchjoy to my life.
Molecular Modeling of
Geochemical Reactions
An Introduction
Edited by
JAMES D. KUBICKI
University of Texas at El Paso, USA
Thiseditionfirstpublished2016
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1 2016
Contents
List of Contributors xi
Preface xiii
1 Introduction to the Theoryand Methods of Computational Chemistry 1
David M. Sherman
1.1 Introduction 1
1.2 Essentials ofQuantum Mechanics 2
1.2.1 The Schrödinger Equation 4
1.2.2 Fundamental Examples 4
1.3 Multielectronic Atoms 7
1.3.1 The Hartree and Hartree–Fock Approximations 7
1.3.2 Density Functional Theory 13
1.4 Bonding in Molecules and Solids 17
1.4.1 The Born–Oppenheimer Approximation 17
1.4.2 Basis Sets and theLinearCombinationof Atomic Orbital Approximation 18
1.4.3 Periodic BoundaryConditions 20
1.4.4 Nuclear Motions and Vibrational Modes 21
1.5 From Quantum Chemistry to Thermodynamics 22
1.5.1 Molecular Dynamics 24
1.6 Available Quantum Chemistry Codes and Their Applications 27
References 28
2 Force Field Application and Development 33
Marco Molinari,Andrey V. Brukhno, Stephen C.Parker, andDino Spagnoli
2.1 Introduction 33
2.2 Potential Forms 35
2.2.1 The Non-bonded Interactions 35
2.2.2 The Bonded Interactions 37
2.2.3 PolarisationEffects 37
2.2.4 Reactivity 39
2.2.5 Fundamentals of Coarse Graining 40
2.3 Fitting Procedure 42
2.3.1 Combining Rules BetweenUnlike Species 42
2.3.2 OptimisationProceduresfor All-Atom Force Fields 43
2.3.3 Deriving CG Force Fields 45
2.3.4 Accuracy and Limitations ofthe Fitting 47
2.3.5 Transferability 48
vi Contents
2.4 Force Field Libraries 48
2.4.1 General Force Fields 48
2.4.2 Force Field Libraries forOrganics: Biomolecules with Minerals 49
2.4.3 Potentials for theAqueous Environment 50
2.4.4 CurrentCGFF Potentials 51
2.4.5 Multi-scale Methodologies 53
2.5 Evolution of Force Fields for Selected Classes of Minerals 54
2.5.1 Calcium Carbonate 54
2.5.2 Clay Minerals 56
2.5.3 Hydroxides and Hydrates 60
2.5.4 Silicaand Silicates 60
2.5.5 Iron-Based Minerals 61
2.6 Concluding Remarks 63
References 64
3 Quantum-Mechanical Modeling of Minerals 77
AlessandroErba and Roberto Dovesi
3.1 Introduction 77
3.2 Theoretical Framework 79
3.2.1 Translation Invariance and Periodic BoundaryConditions 79
3.2.2 HF and KS Methods 80
3.2.3 BlochFunctions and Local BS 81
3.3 Structural Properties 82
3.3.1 P–V Relation Through Analytical Stress Tensor 83
3.3.2 P–V Relation Through Equation ofState 85
3.4 Elastic Properties 86
3.4.1 Evaluation of the Elastic Tensor 86
3.4.2 Elastic Tensor-Related Properties 89
3.4.3 Directional Seismic Wave Velocities and Elastic Anisotropy 89
3.5 Vibrational and Thermodynamic Properties 91
3.5.1 Solid-State Thermodynamics 93
3.6 Modeling Solid Solutions 95
3.7 Future Challenges 98
References 99
4 First Principles Estimation of Geochemically ImportantTransition MetalOxide
Properties: Structure and Dynamics of the Bulk, Surface, and Mineral/Aqueous
Fluid Interface 107
Ying Chen, Eric Bylaska, and John Weare
4.1 Introduction 107
4.2 Overview of theTheoretical Methods and Approximations Needed toPerform
AIMD Calculations 109
4.3 Accuracy of Calculations for Observable Bulk Properties 113
4.3.1 BulkStructural Properties 113
4.3.2 BulkElectronic Structure Properties 118
4.4 Calculation of Surface Properties 123
4.4.1 Surface Structural Properties 123
Contents vii
4.4.2 Electronic Structurein the Surface Region 127
4.4.3 Water Adsorption on Surface 129
4.5 Simulations of theMineral–Water Interface 130
4.5.1 CPMD Simulations of the Vibrational Structureof the Hematite
(012)–Water Interface 130
4.5.2 CPMD Simulations of Fe2+Species at the Mineral–Water Interface 132
4.6 Future Perspectives 134
Acknowledgments 134
Appendix 134
A.1 ShortIntroduction toPseudopotentials 135
A.1.1 The Spin Penalty Pseudopotential 137
A.1.2 Projected Density of States from Pseudo-Atomic Orbitals 138
A.2 Hubbard-Like Coulomb and Exchange (DFT+U) 138
A.3 Overviewof the PAW Method 139
References 143
5 ComputationalIsotope Geochemistry 151
James R.Rustad
5.1 A Brief Statement ofElectronic Structure Theoryand theElectronic Problem 152
5.2 The Vibrational Eigenvalue Problem 154
5.3 Isotope Exchange Equilibria 156
5.4 Qualitative Insights 159
5.5 Quantitative Estimates 160
5.6 Relationship to Empirical Estimates 169
5.7 Beyondthe Harmonic Approximation 171
5.8 Kinetic Isotope Effects 172
5.9 Summaryand Prognosis 172
Acknowledgments 173
References 173
6 Organic and Contaminant Geochemistry 177
Daniel Tunega, Martin H. Gerzabek,Georg Haberhauer,Hans Lischka,
andAdelia J. A.Aquino
6.1 Introduction 177
6.1.1 Review Examples ofMolecular Modeling Applications in Organic
and Contaminant Geochemistry 179
6.2 Molecular Modeling Methods 184
6.2.1 Molecular Mechanics: Brief Summary 184
6.2.2 Quantum Mechanics: Overview 187
6.2.3 Molecular Modeling Techniques: Summary 192
6.2.4 Models: Clusters, Periodic Systems, and Environmental Effects 195
6.3 Applications 196
6.3.1 Modeling of Surface Complexesof Polar Phenoxyacetic Acid-Based
Herbicides with Iron Oxyhydroxidesand Clay Minerals 197
6.3.2 Modeling of Adsorption Processes of Polycyclic Aromatic Hydrocarbons
on Iron Oxyhydroxides 217
viii Contents
6.3.3 Modeling of Interactions ofPolar and Nonpolar Contaminants in Organic
Geochemical Environment 220
6.4 Perspectives and Future Challenges 227
Glossary 229
References 231
7 Petroleum Geochemistry 245
Qisheng Ma and Yongchun Tang
7.1 Introduction: Petroleum Geochemistryand Basin Modeling 245
7.2 TechnologyDevelopmentof the Petroleum Geochemistry 246
7.2.1 Thermal Maturity and Vitrinite Reflectance 246
7.2.2 Rock-Eval Pyrolysis 247
7.2.3 Kerogen Pyrolysis and GasChromatography Analysis 248
7.2.4 Kinetic Modeling of Kerogen Pyrolysis 249
7.2.5 Natural Gases and C/HIsotopes 253
7.3 ComputationalSimulations in Petroleum Geochemistry 253
7.3.1 Ab Initio Calculations of theUnimolecular C–C Bond Rapture 253
7.3.2 Quantum Mechanical Calculations on Natural Gas13C Isotopic Fractionation 256
7.3.3 Deuterium Isotope Fractionations of Natural Gas 258
7.3.4 Molecular Modeling ofthe 13C and D Doubly Substituted Methane Isotope 260
7.4 Summary 262
References 262
8 Mineral–Water Interaction 271
Marie-Pierre Gaigeot and Marialore Sulpizi
8.1 Introduction 271
8.2 Brief Review of AIMD Simulation Method 275
8.2.1 Ab Initio Molecular Dynamics and Density Functional Theory 275
8.3 Calculation of theSurface Acidity from Reversible Proton Insertion/Deletion 280
8.4 Theoretical Methodology for Vibrational Spectroscopyand Mode Assignments 282
8.5 Property Calculations from AIMD:Dipoles and Polarisabilities 284
8.6 Illustrationsfrom OurRecent Works 286
8.6.1 Organisation of Water at Silica–Water Interfaces: (0001) α-Quartz Versus
Amorphous Silica 286
8.6.2 Organisation of Water at Alumina–Water Interface: (0001) α-Alumina
Versus (101) Boehmite 291
8.6.3 How Surface Acidities Dictate the Interfacial WaterStructural
Arrangement 293
8.6.4 VibrationalSpectroscopy at Oxide–Liquid Water Interfaces 295
8.6.5 Clay–Water Interface: Pyrophyllite and Calcium Silicate 299
8.7 Some Perspectives for Future Works 302
References 304
9 Biogeochemistry 311
Weilong Zhao, Zhijun Xu, and Nita Sahai
9.1 Introduction 311
9.1.1 Mineral–Water Interactions 313
9.1.2 Mineral–Organic Interactions 313
Contents ix
9.2 Challengesand Approaches to Computational Modeling of Biomineralization 314
9.2.1 Biominerals: Structure, Nucleation, and Growth 314
9.2.2 ConformationalSampling in ModelingBiomineralization 317
9.2.3 Force Field Benchmarking 324
9.2.4 Ab Initio MD and Hybrid QM/MMApproaches 325
9.3 Case Studies 326
9.3.1 Apatite 327
9.3.2 Calcite 331
9.4 Concluding Remarks and Future Perspectives 334
Acknowledgments 335
References 335
10 Vibrational Spectroscopy of Minerals Through Ab Initio Methods 341
Marco De LaPierre, Raffaella Demichelis, andRoberto Dovesi
10.1 Introduction 341
10.2 Theoretical Background and Methods 342
10.2.1 Calculation of Vibrational Frequencies 344
10.2.2 Splitting ofthe Longitudinal Optical (LO) and Transverse Optical (TO)
Modes 346
10.2.3 Calculation of Infrared (IR) and Raman Peak Intensities and of the
IR Dielectric Function 347
10.2.4 Estimation of the Anharmonic Constant for X–H Stretching Modes 349
10.2.5 Accuracy of Basis Set and Hamiltonian 350
10.3 Examples and Applications 352
10.3.1 Vibrational Properties ofCalcium and Magnesium Carbonates 353
10.3.2 A ComplexMineral: The IR Spectra of Ortho-enstatite 359
10.3.3 Treatment ofthe O─H Stretching Modes:The Vibrational Spectra
of Brucite and Diaspore 360
10.4 Simulation of Vibrational Properties forCrystal Structure Determination 363
10.4.1 Proton Disorder in γ-AlOOH Boehmite 364
10.5 Future Challenges 368
Acknowledgements 368
References 368
11 Geochemical Kinetics via ComputationalChemistry 375
James D.Kubicki andKevin M. Rosso
11.1 Introduction 375
11.2 Methods 379
11.2.1 Potential Energy Surfaces 379
11.2.2 Choice of Solvation Methods 384
11.2.3 Activation Energies and Volumes 386
11.2.4 Transition States and Imaginary Frequencies 390
11.2.5 Rate Constants 391
11.2.6 Types of Reaction Mechanisms 393
11.3 Applications 394
11.3.1 Diffusion 394
11.3.2 Ligand Exchange Aqueous Complexes 395
11.3.3 Adsorption 396
x Contents
11.3.4 Dissolution 396
11.3.5 Nucleation 398
11.4 Future Challenges 399
11.4.1 FemtosecondSpectroscopy 399
11.4.2 H-Bonding 400
11.4.3 Roaming 400
11.4.4 Large-Scale Quantum Molecular Dynamics 401
11.4.5 Reactive Force Fields 401
References 403
Index 415